I record all my audio direct to Pro Tools. I record 3 tracks. Once I'm done, my video editor wants me to send him 1 reference track for the video edits.Once he finished his edits, he sends me an AAF file with the edited audio.

The problem with this is that I only get back one "edited" audio track. It's easier for them to only have 1 audio track instead of messing with 3.

Is there any way to link my 3 "raw" audio tracks so they will line up/follow the edited AAF i am given?

I'm guessing this might work..
If your audio files are recorded in broadcast wave format, they should have timecode burnt into the metadata..
After you import the track the editor gives you, right click on it and choose 'Expand channel to new tracks' > 'By timecode only'.. This should retrieve all the individual tracks with the edits..
BTW this can only work if the tracks were recorded on the same day in Pro Tools.. Otherwise there will be a conflict in the timecode..

Option 1) export your tracks as an AAF, and kindly ask your editor to cut those, what is not a big deal at all... Then you`ll get the edited version back in full.
Option 2) get the reference track from the editor, and use PT Guide Track function to line your other tracks up, you just need HD license for this.

Yes, this is what I've been told. By two other audio editors.
The problem is if you are working on a large production with lots of discreet channels of dialogue, they'll deliver an AAF with just the camera audio, they can't be bothered to bring in all the audio from the audio cards and expect you to do it. I've had this happen. Which is fine if you have a third party conformer. But if you only have field recorder tracks in Pro Tools to work with then your stuck if the haven't maintained all the meta data in the original files.

I'm able to sync up Pro Tools to a master clock so my cameras and now my audio are all synced to the same Timecode. So this will help A LOT in the edting process.

Premiere (i guess) can export an .xml document that has all the cuts that were made in the time code. So will the AAF and the "cut sheet", this should be all i need to be able to maintain my original audio.

So now, what I'm doing, is just giving them a single reference track ,and only mixing in my raw tracks. If the mix needs to be redone, I will remix it and give it back to the editor to re-link it with the video cut. Than do my edits on the mixed track.

I know it seems a little back asswards, but for us it works pretty well. Plus I have the timecode sync ad the AAF edited tracks, so that makes things a little easier.

"I'm able to sync up Pro Tools to a master clock so my cameras and now my audio are all synced to the same Timecode. So this will help A LOT in the edting process"
Did you use an external hardware to do this?
If so, and later if you do a mix inside of Pro Tools and send it to the editor, will you be able to retrieve the individual tracks from the mix track timecode? What I mean is, if you do the mix at a different time after the individual tracks are recorded.